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Index of /EvidentialGene/vertebrates/killifish/Proteins

      Name                    Last modified       Size  

[DIR] Parent Directory 10-Jan-2014 14:45 - [TXT] fish11_info.txt 04-Jan-2014 16:27 2k [DIR] fish11seq/ 04-Jan-2014 16:11 - [DIR] fish12seq/ 23-Mar-2014 20:47 -


Oreochromis niloticus (Tilapia) 
  ftp://ftp.ensembl.org/pub/release-67/fasta/oreochromis_niloticus/pep/

Oryzias latipes (Medaka)  
  ftp://ftp.ensembl.org/pub/release-67/fasta/oryzias_latipes/pep/

Gasterosteus aculeatus (Stickleback) 
  ftp://ftp.ensembl.org/pub/release-67/fasta/gasterosteus_aculeatus/pep/

Tetraodon nigroviridis 
  ftp://ftp.ensembl.org/pub/release-67/fasta/tetraodon_nigroviridis/pep/

Danio rerio (Zebrafish)  
  ftp://ftp.ensembl.org/pub/release-67/fasta/danio_rerio/pep/

Xiphophorus maculatus (Platyfish) - 2012/01/06 
   -- goodish gene set, using 500M rnaseq reads + fish prots
  ftp://ftp.ensembl.org/pub/release-70/fasta/xiphophorus_maculatus/pep/
  www.ensembl.org/Xiphophorus_maculatus/Info/Annotation/
  
Lepisosteus_oculatus  (spotted gar)
  -- poor, prelim gene set, only mapped proteins of other fish
  http://www.ensembl.info/blog/2012/04/24/new-pre-sites-for-painted-turtle-and-spotted-gar/
  http://pre.ensembl.org/Lepisosteus_oculatus/Info/Index

Ictalurus punctatus (catfish) 
  mRNA Transcript assemblies with EvidentialGene (2013 Jan) 
  http://arthropods.eugenes.org/EvidentialGene/vertebrates/catfish/catfish1eg6/

Maylandia zebra  (mayzebr, african cichlid)
  ncbi: genomes/Maylandia_zebra/protein/protein.fa.gz 2013/05

Human, from UniProt UniRef50 2013 May. 39357 proteins (9408 fragments excluded)

N proteins used for orthology:
alternate isoforms were removed, where identified (zfish,platyfish,ensembl-genes)

43671 catfish (main set of 118588 isoforms)
39357 human   (UniRef50 main set)
34932 kfish2  (kfish2rae5g.main version, of 114000 isoforms)
23194 mayzebr (main of 38798 isoforms)
19686 medaka  (main of 24661 isoforms)
20366 platyfish (main of 20441 isoforms)
15734 spotgar	(90% cd-cluster of 39913 isoforms)
20787 stickleback (main of 27576 isoforms)
19602 tetraodon (main of nnn isoforms)
21437 tilapia (main of 26763 isoforms)
26190 zfish   (main set of 41667 isoforms)
------------
284956 total


Developed at the Genome Informatics Lab of Indiana University Biology Department